HIV-1, like other retroviruses, is recombinogenic as a consequence of its dimeric genome and an RT that can switch between templates during proviral DNA synthesis. Hybrid genomes can be generated when two parental genomes are copackaged within the same cell. A review has described 11 CRFs, defined as completely sequenced recombinant isolates infecting at least two epidemiologically unrelated individuals. Two of these CRFs (CRF01_AE and CRF02_AG) are highly prevalent and play a major role in the HIV-1 pandemic.
CRFs are most likely to occur in Africa, where there are multiple circulating subtypes, high rates of infection and, in some cases, dual infection. HIV-1 subtypes A and D are common, making it likely that some individuals will be dually infected and at risk for developing recombinant viruses. Systemic sampling of HIV-1 from 102 epidemiologically unrelated Ugandan women provides a minimum estimate of intersubtype recombination in the population studied. Although 13% of the women had strong evidence of being infected with recombinant viruses, the actual prevalence that would be revealed by complete genome sequencing of the isolates may in fact be higher.
The fact that nine of the women had the same recombinant identified at two points in time, and that five of the women transmitted a recombinant virus perinatally, confirms that these recombinant isolates do not represent polymerase chain reaction (PCR) artifacts and also demonstrates the stability of these variants in vivo. The fact that three different recombinant forms were present in at least two women suggests that these recombinants may be common variants in parts of Uganda. These variants, however, cannot be considered CRFs because their whole genomes were not sequenced.
Although previous studies have shown that hybrid pol proteins can be formed, the multiple patterns of recombination observed in the 13 isolates in this study suggest that many parts of the RT gene are possible sites for recombination. Our analysis also highlights some of the difficulties faced by the programs used to detect recombination within pol. The pol gene is less variable than env and parts of gag and therefore has fewer phylogenetically informative sites. Applying such programs as RIP and SimPlot without examining the bootstrap support for putative sites of recombination often shows weak evidence for recombination in isolates that are probably not recombinant. Strong evidence of recombination in pol should therefore require using a larger window size (e.g., 400 bp) and should be supported by high bootscan support (90-100%) in regions of recombination.
Intersubtype recombination provides a powerful mechanism for adaptive HIV-1 evolution. Such recombination within the pol gene may increase the rapidity with which multidrug-resistant HIV-1 isolates are generated. The use of antiretroviral drug therapy in regions with a high prevalence of HIV-1 infection should be coupled with efforts to prevent ongoing HIV-1 transmissions to reduce the risk of dual infection and the generation of new recombinant forms. Intersubtype recombination also complicates efforts aimed at classifying sequenced isolates, particularly in the more conserved regions of the HIV-1 genome such as those encoding the molecular targets of HIV-1 therapy.